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gad-public
vihgo
Commits
552afefb
Commit
552afefb
authored
Jul 10, 2020
by
Yannis Duffourd
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in run control is now an option
parent
4ca3fb2b
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7 additions
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5 deletions
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-5
main.cpp
cpp/main.cpp
+7
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cpp/main.cpp
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552afefb
...
...
@@ -18,6 +18,7 @@
// Classes
#include "Vihgo.h"
using
namespace
std
;
namespace
po
=
boost
::
program_options
;
...
...
@@ -157,11 +158,7 @@ int main(int argc, char* argv[])
return
-
1
;
}
}
else
{
cerr
<<
"No file provided as control sample BAM file : stopping"
<<
endl
;
return
-
1
;
}
if
(
geneFile
.
length
(
)
>
0
)
{
...
...
@@ -178,6 +175,11 @@ int main(int argc, char* argv[])
}
if
(
vm
.
count
(
"stop"
)
)
{
countStop
=
true
;
}
Vihgo
*
App
=
new
Vihgo
(
bamFile
,
geneFile
,
rtFile
,
integraseFile
,
proteaseFile
,
referenceFile
,
outputFile
,
codonResultFile
,
csFile
,
inRunControlBam
,
depthThreshold
,
nbThread
,
loggingLevel
,
ratioThreshold
,
pvalueThreshold
,
countStop
);
App
->
mainLoop
();
...
...
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